My little mantra again I you don't mind - you want to be able to choose. For an early stage player, following the technical approach of an early composer is not normally recommended, simply because we assume you will want to play other repertoires, and to train oneself to play like, e.g. Sor, will not be as helpful as one would wish.
I always get people to use the thumb for whatever is meant to sound like a bass note, and only use it for other voices if there really is no time for anything else. So if you think of a piece as being like an ensemble, perhaps a vocal or string ensemble, there is only one actual bass performer, and they typically have a characteristic bassiness of tone. This is handily (pun intended) supplied by the thumb. So if in Op 35 no 2 we look at the second section, we find that the down-tailed bass note is followed by a down-tailed middle voice in several bars. Using the thumb for that middle voice would defeat the object of communicating the bass tone where it really should be.
Btw stem direction in middle voices esp is often determined by graphical convenience rather than actual musical considerations. So in Op 35 no 1, the middle voice Gs are very like those in no 2, but are stemmed upwards (actually the no 2 Gs have double tails but the principle remains, and other examples may be clearer, e.g. op 31 no 1).
Coming back to the thing of being able to choose; try to make sure that decisions such as this are driven first by conscious decision, and try to make that decision on a musical basis e.g. in terms of the sound you make. And seek at your stage to do so in a 'modern' manner, so that if in future you want to specialise in another approach, or adopt another approach for particular repertoires, you can choose to do so.
Simon Ambridge Series 40 (2005)
Trevor Semple Series 88 (1992)
Louis Panormo (1838)
Alexander Batov Baroque Guitar (2013)